public static void TestAllNaN() { IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >(); var prot = new Protein("XMMM", null, null, null, mods); DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1); var thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First(); var frags = new List <Product>(); thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags); var massArray = frags.Select(p => p.NeutralMass).ToArray(); Array.Sort(massArray); double[] intensities = new double[] { 1, 1, 1, 1 }; double[] mz = new double[] { 1, 2, 3, 4 }; MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false); MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null); PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1]; Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null, new CommonParameters()) }; CommonParameters CommonParameters = new CommonParameters(productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: int.MaxValue, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)); ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, null, null, new List <Protein> { prot }, new OpenSearchMode(), CommonParameters, null, new List <string>()); cse.Run(); Assert.IsNull(globalPsms[0]); }
public static void TestIdenticalPeaks() { IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >(); ModificationMotif.TryGetMotif("M", out ModificationMotif motif); mods.Add(1, new List <Modification> { new ModificationWithMass("Hehe", null, motif, TerminusLocalization.NProt, 18.010565, null, null, null, null) }); var prot = new Protein("MMMM", null, null, null, mods); DigestionParams digestionParams = new DigestionParams { MinPeptideLength = 1, }; var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First(); var massArray = ye.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { ProductType.B, ProductType.Y }); Array.Sort(massArray); double[] intensities = new double[] { 1, 1, 1, 1 }; double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 }; MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false); IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1"); PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1]; Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) }; CommonParameters CommonParameters = new CommonParameters { DigestionParams = new DigestionParams { MaxMissedCleavages = 0, MinPeptideLength = null, MaxModificationIsoforms = int.MaxValue, InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain, }, ProductMassTolerance = new PpmTolerance(5), ConserveMemory = false, ScoreCutoff = 1 }; ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> { prot }, new List <ProductType> { ProductType.B, ProductType.Y }, new OpenSearchMode(), false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()); cse.Run(); Assert.Less(globalPsms[0].Score, 4); Assert.Greater(globalPsms[0].Score, 3); }
public static void TestIdenticalPeaks() { IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >(); ModificationMotif.TryGetMotif("M", out ModificationMotif motif); mods.Add(1, new List <Modification> { new Modification(_originalId: "Hehe", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 18.010565) }); var prot = new Protein("MMMM", null, null, null, mods); DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1); var ye = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First(); var frags = new List <Product>(); ye.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags); var massArray = frags.Select(p => p.NeutralMass).ToArray(); Array.Sort(massArray); double[] intensities = new double[] { 1, 1, 1, 1 }; double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 }; MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false); MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null); PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1]; Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 1, null, new CommonParameters()) }; CommonParameters CommonParameters = new CommonParameters( productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams( maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)); bool writeSpectralLibrary = false; ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, null, null, new List <Protein> { prot }, new OpenSearchMode(), CommonParameters, null, null, new List <string>(), writeSpectralLibrary); cse.Run(); Assert.AreEqual(3, globalPsms[0].MatchedFragmentIons.Count); }
public static void TestIdenticalPeaks() { IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >(); ModificationMotif.TryGetMotif("M", out ModificationMotif motif); mods.Add(1, new List <Modification> { new ModificationWithMass("Hehe", null, motif, TerminusLocalization.NProt, 18.010565, null, null, null, null) }); var prot = new Protein("MMMM", null, null, null, mods); DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1); var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First(); var massArray = ye.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { ProductType.B, ProductType.Y }); Array.Sort(massArray); double[] intensities = new double[] { 1, 1, 1, 1 }; double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 }; MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false); MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null); PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1]; Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) }; CommonParameters CommonParameters = new CommonParameters( productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams( maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)); ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> { prot }, new List <ProductType> { ProductType.B, ProductType.Y }, new OpenSearchMode(), CommonParameters, new List <string>()); cse.Run(); Assert.AreEqual(globalPsms[0].MatchedFragmentIons.Count, 3); }
public static void TestVeryCloseExperimentalsClassic() { IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >(); ModificationMotif.TryGetMotif("M", out ModificationMotif motif); var prot = new Protein("MMMM", null, null, null, mods); DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1); var thePep = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First(); var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { ProductType.B, ProductType.Y }); Array.Sort(massArray); double[] intensities = new double[] { 1, 1, 1, 1 }; double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 }; MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false); MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null); PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1]; Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) }; CommonParameters CommonParameters = new CommonParameters( productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams( maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: int.MaxValue, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)); ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> { prot }, new List <ProductType> { ProductType.B, ProductType.Y }, new OpenSearchMode(), CommonParameters, new List <string>()); cse.Run(); Assert.Less(globalPsms[0].Score, 2); Assert.Greater(globalPsms[0].Score, 1); }
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList) { if (SearchParameters.DoQuantification) { // disable quantification if a .mgf is being used if (currentRawFileList.Any(x => Path.GetExtension(x).Equals(".mgf", StringComparison.OrdinalIgnoreCase))) { SearchParameters.DoQuantification = false; } //if we're doing SILAC, assign and add the silac labels to the residue dictionary else if (SearchParameters.SilacLabels != null || SearchParameters.StartTurnoverLabel != null || SearchParameters.EndTurnoverLabel != null) { char heavyLabel = 'a'; //char to assign //add the Turnoverlabels to the silacLabels list. They weren't there before just to prevent duplication in the tomls if (SearchParameters.StartTurnoverLabel != null || SearchParameters.EndTurnoverLabel != null) { //original silacLabels object is null, so we need to initialize it SearchParameters.SilacLabels = new List <SilacLabel>(); if (SearchParameters.StartTurnoverLabel != null) { var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.StartTurnoverLabel, heavyLabel); heavyLabel = updatedLabel.nextHeavyLabel; SearchParameters.StartTurnoverLabel = updatedLabel.updatedLabel; SearchParameters.SilacLabels.Add(SearchParameters.StartTurnoverLabel); } if (SearchParameters.EndTurnoverLabel != null) { var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.EndTurnoverLabel, heavyLabel); heavyLabel = updatedLabel.nextHeavyLabel; SearchParameters.EndTurnoverLabel = updatedLabel.updatedLabel; SearchParameters.SilacLabels.Add(SearchParameters.EndTurnoverLabel); } } else { //change the silac residues to lower case amino acids (currently null) List <SilacLabel> updatedLabels = new List <SilacLabel>(); for (int i = 0; i < SearchParameters.SilacLabels.Count; i++) { var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.SilacLabels[i], heavyLabel); heavyLabel = updatedLabel.nextHeavyLabel; updatedLabels.Add(updatedLabel.updatedLabel); } SearchParameters.SilacLabels = updatedLabels; } } } //if no quant, remove any silac labels that may have been added, because they screw up downstream analysis if (!SearchParameters.DoQuantification) //using "if" instead of "else", because DoQuantification can change if it's an mgf { SearchParameters.SilacLabels = null; } LoadModifications(taskId, out var variableModifications, out var fixedModifications, out var localizeableModificationTypes); // load proteins List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, SearchParameters.SearchTarget, SearchParameters.DecoyType, localizeableModificationTypes, CommonParameters); SanitizeProteinDatabase(proteinList, SearchParameters.TCAmbiguity); // load spectral libraries var spectralLibrary = LoadSpectralLibraries(taskId, dbFilenameList); // write prose settings ProseCreatedWhileRunning.Append("The following search settings were used: "); ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; "); ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; "); ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; "); ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "maximum peptide length = unspecified; " : "maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; "); ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; "); ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.IdWithMotif)) + "; "); ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.IdWithMotif)) + "; "); ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; "); ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; "); ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; "); ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + "; "); ProseCreatedWhileRunning.Append("report PSM ambiguity = " + CommonParameters.ReportAllAmbiguity + ". "); ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. "); // start the search task MyTaskResults = new MyTaskResults(this); List <PeptideSpectralMatch> allPsms = new List <PeptideSpectralMatch>(); //generate an array to store category specific fdr values (for speedy semi/nonspecific searches) int numFdrCategories = (int)(Enum.GetValues(typeof(FdrCategory)).Cast <FdrCategory>().Last() + 1); //+1 because it starts at zero List <PeptideSpectralMatch>[] allCategorySpecificPsms = new List <PeptideSpectralMatch> [numFdrCategories]; for (int i = 0; i < numFdrCategories; i++) { allCategorySpecificPsms[i] = new List <PeptideSpectralMatch>(); } FlashLfqResults flashLfqResults = null; MyFileManager myFileManager = new MyFileManager(SearchParameters.DisposeOfFileWhenDone); var fileSpecificCommonParams = fileSettingsList.Select(b => SetAllFileSpecificCommonParams(CommonParameters, b)); int completedFiles = 0; object indexLock = new object(); object psmLock = new object(); Status("Searching files...", taskId); Status("Searching files...", new List <string> { taskId, "Individual Spectra Files" }); Dictionary <string, int[]> numMs2SpectraPerFile = new Dictionary <string, int[]>(); for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++) { if (GlobalVariables.StopLoops) { break; } var origDataFile = currentRawFileList[spectraFileIndex]; // mark the file as in-progress StartingDataFile(origDataFile, new List <string> { taskId, "Individual Spectra Files", origDataFile }); CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]); MassDiffAcceptor massDiffAcceptor = GetMassDiffAcceptor(combinedParams.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac); var thisId = new List <string> { taskId, "Individual Spectra Files", origDataFile }; NewCollection(Path.GetFileName(origDataFile), thisId); Status("Loading spectra file...", thisId); MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams); Status("Getting ms2 scans...", thisId); Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams).OrderBy(b => b.PrecursorMass).ToArray(); numMs2SpectraPerFile.Add(Path.GetFileNameWithoutExtension(origDataFile), new int[] { myMsDataFile.GetAllScansList().Count(p => p.MsnOrder == 2), arrayOfMs2ScansSortedByMass.Length }); myFileManager.DoneWithFile(origDataFile); PeptideSpectralMatch[] fileSpecificPsms = new PeptideSpectralMatch[arrayOfMs2ScansSortedByMass.Length]; // modern search if (SearchParameters.SearchType == SearchType.Modern) { for (int currentPartition = 0; currentPartition < combinedParams.TotalPartitions; currentPartition++) { List <PeptideWithSetModifications> peptideIndex = null; List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count / combinedParams.TotalPartitions)); Status("Getting fragment dictionary...", new List <string> { taskId }); var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, SearchParameters.SilacLabels, SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, currentPartition, SearchParameters.DecoyType, combinedParams, FileSpecificParameters, SearchParameters.MaxFragmentSize, false, dbFilenameList.Select(p => new FileInfo(p.FilePath)).ToList(), SearchParameters.TCAmbiguity, new List <string> { taskId }); List <int>[] fragmentIndex = null; List <int>[] precursorIndex = null; lock (indexLock) { GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, ref precursorIndex, proteinList, taskId); } Status("Searching files...", taskId); new ModernSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, currentPartition, combinedParams, this.FileSpecificParameters, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run(); ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + combinedParams.TotalPartitions + "!", thisId)); if (GlobalVariables.StopLoops) { break; } } } // nonspecific search else if (SearchParameters.SearchType == SearchType.NonSpecific) { PeptideSpectralMatch[][] fileSpecificPsmsSeparatedByFdrCategory = new PeptideSpectralMatch[numFdrCategories][]; //generate an array of all possible locals for (int i = 0; i < numFdrCategories; i++) //only add if we're using for FDR, else ignore it as null. { fileSpecificPsmsSeparatedByFdrCategory[i] = new PeptideSpectralMatch[arrayOfMs2ScansSortedByMass.Length]; } //create params for N, C, or both if semi List <CommonParameters> paramsToUse = new List <CommonParameters> { combinedParams }; if (combinedParams.DigestionParams.SearchModeType == CleavageSpecificity.Semi) //if semi, we need to do both N and C to hit everything { paramsToUse.Clear(); List <FragmentationTerminus> terminiToUse = new List <FragmentationTerminus> { FragmentationTerminus.N, FragmentationTerminus.C }; foreach (FragmentationTerminus terminus in terminiToUse) //set both termini { paramsToUse.Add(combinedParams.CloneWithNewTerminus(terminus)); } } //Compress array of deconvoluted ms2 scans to avoid searching the same ms2 multiple times while still identifying coisolated peptides List <int>[] coisolationIndex = new List <int>[] { new List <int>() }; if (arrayOfMs2ScansSortedByMass.Length != 0) { int maxScanNumber = arrayOfMs2ScansSortedByMass.Max(x => x.OneBasedScanNumber); coisolationIndex = new List <int> [maxScanNumber + 1]; for (int i = 0; i < arrayOfMs2ScansSortedByMass.Length; i++) { int scanNumber = arrayOfMs2ScansSortedByMass[i].OneBasedScanNumber; if (coisolationIndex[scanNumber] == null) { coisolationIndex[scanNumber] = new List <int> { i }; } else { coisolationIndex[scanNumber].Add(i); } } coisolationIndex = coisolationIndex.Where(x => x != null).ToArray(); } //foreach terminus we're going to look at foreach (CommonParameters paramToUse in paramsToUse) { //foreach database partition for (int currentPartition = 0; currentPartition < paramToUse.TotalPartitions; currentPartition++) { List <PeptideWithSetModifications> peptideIndex = null; List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count / paramToUse.TotalPartitions, ((currentPartition + 1) * proteinList.Count / paramToUse.TotalPartitions) - (currentPartition * proteinList.Count / paramToUse.TotalPartitions)); List <int>[] fragmentIndex = null; List <int>[] precursorIndex = null; Status("Getting fragment dictionary...", new List <string> { taskId }); var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, SearchParameters.SilacLabels, SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, currentPartition, SearchParameters.DecoyType, paramToUse, FileSpecificParameters, SearchParameters.MaxFragmentSize, true, dbFilenameList.Select(p => new FileInfo(p.FilePath)).ToList(), SearchParameters.TCAmbiguity, new List <string> { taskId }); lock (indexLock) { GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, ref precursorIndex, proteinList, taskId); } Status("Searching files...", taskId); new NonSpecificEnzymeSearchEngine(fileSpecificPsmsSeparatedByFdrCategory, arrayOfMs2ScansSortedByMass, coisolationIndex, peptideIndex, fragmentIndex, precursorIndex, currentPartition, paramToUse, this.FileSpecificParameters, variableModifications, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run(); ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + paramToUse.TotalPartitions + "!", thisId)); if (GlobalVariables.StopLoops) { break; } } } lock (psmLock) { for (int i = 0; i < allCategorySpecificPsms.Length; i++) { if (allCategorySpecificPsms[i] != null) { allCategorySpecificPsms[i].AddRange(fileSpecificPsmsSeparatedByFdrCategory[i]); } } } } // classic search else { Status("Starting search...", thisId); var newClassicSearchEngine = new ClassicSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, variableModifications, fixedModifications, SearchParameters.SilacLabels, SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, proteinList, massDiffAcceptor, combinedParams, this.FileSpecificParameters, spectralLibrary, thisId, SearchParameters.WriteSpectralLibrary); newClassicSearchEngine.Run(); ReportProgress(new ProgressEventArgs(100, "Done with search!", thisId)); } //look for internal fragments if (SearchParameters.MinAllowedInternalFragmentLength != 0) { MatchInternalFragmentIons(fileSpecificPsms, arrayOfMs2ScansSortedByMass, combinedParams, SearchParameters.MinAllowedInternalFragmentLength); } // calculate/set spectral angles if there is a spectral library being used if (spectralLibrary != null) { Status("Calculating spectral library similarity...", thisId); } SpectralLibrarySearchFunction.CalculateSpectralAngles(spectralLibrary, fileSpecificPsms, arrayOfMs2ScansSortedByMass, combinedParams); lock (psmLock) { allPsms.AddRange(fileSpecificPsms); } completedFiles++; FinishedDataFile(origDataFile, new List <string> { taskId, "Individual Spectra Files", origDataFile }); ReportProgress(new ProgressEventArgs(completedFiles / currentRawFileList.Count, "Searching...", new List <string> { taskId, "Individual Spectra Files" })); } if (spectralLibrary != null) { spectralLibrary.CloseConnections(); } ReportProgress(new ProgressEventArgs(100, "Done with all searches!", new List <string> { taskId, "Individual Spectra Files" })); int numNotches = GetNumNotches(SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac); //resolve category specific fdrs (for speedy semi and nonspecific if (SearchParameters.SearchType == SearchType.NonSpecific) { allPsms = NonSpecificEnzymeSearchEngine.ResolveFdrCategorySpecificPsms(allCategorySpecificPsms, numNotches, taskId, CommonParameters, FileSpecificParameters); } PostSearchAnalysisParameters parameters = new PostSearchAnalysisParameters { SearchTaskResults = MyTaskResults, SearchTaskId = taskId, SearchParameters = SearchParameters, ProteinList = proteinList, AllPsms = allPsms, VariableModifications = variableModifications, FixedModifications = fixedModifications, ListOfDigestionParams = new HashSet <DigestionParams>(fileSpecificCommonParams.Select(p => p.DigestionParams)), CurrentRawFileList = currentRawFileList, MyFileManager = myFileManager, NumNotches = numNotches, OutputFolder = OutputFolder, IndividualResultsOutputFolder = Path.Combine(OutputFolder, "Individual File Results"), FlashLfqResults = flashLfqResults, FileSettingsList = fileSettingsList, NumMs2SpectraPerFile = numMs2SpectraPerFile, DatabaseFilenameList = dbFilenameList }; PostSearchAnalysisTask postProcessing = new PostSearchAnalysisTask { Parameters = parameters, FileSpecificParameters = this.FileSpecificParameters, CommonParameters = CommonParameters }; return(postProcessing.Run()); }